Chris Gorgolewski

Online templates

3

As suggested by Trey Smith https://docs.google.com/document/d/1HFUkAEE-pB-angVcYe6pf_-fVf4sCpOHKesUvfb8Grc/edit?disco=AAAABBoxE28 > Here's something that would help JSON novices: for each type of JSON object you describe in your specification, provide a URL to a...

AssertionError on WSL1

2

Getting the same thing on WSL (with current master): ``` (base) me@christop:~/workspace/nibabel$ PYTHONPATH=. nosetests -s -v nibabel/tests/test_floating.py nibabel.tests.test_floating.test_type_info ... ok nibabel.tests.test_floating.test_nmant ... ok nibabel.tests.test_floating.test_check_nmant_nexp ... /home/me/workspace/nibabel/nibabel/casting.py:360: RuntimeWarning: overflow encountered in...

on ds000009 R2.0.1 - sub-29 ``` docker run -ti -v D:\:/d bids/broccoli:v1.0.1 /d/data/ds000009_R2.0.1/ /d/scratch/broccoli participant --participant_label 29 Running the BIDS validator for the dataset 1: Not all subjects/sessions/runs have the...

Noisy T1w leads to poor tissue segmentation

13

 ds000105/reportlets/fmriprep/sub-5/anat/sub-5_T1w_seg_brainmask.svg This could be solved by applying a denoising algorithm: https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging/mri-denoising Implemneted as `DenoiseImage` in ANTs

Wrong T1w mask used for EPI-T1 registration?

2

The T1w mask on bbr coregisration plot looks bad  ds000221/reportlets/fmriprep/sub-010251/ses-01/func/sub-010251_ses-01_task-rest_acq-AP_run-01_bold_bbr.svg Even though it's good on the T1w mask plot  s000221/reportlets/fmriprep/sub-010251/ses-01/anat/sub-010251_ses-01_acq-mp2rage_T1w_seg_brainmask.svg

Add visualizations of surface coregistration (to fsaverage)

3

 https://twitter.com/michaelwaskom/status/963497405726580736

Surface reconstruction failure

2

 Could be poor data or INU failure. sub-12

In case T2w is not present generate it from T1w

1

Using https://github.com/uw-biomedical-ml/mri2mri

Gene enrichment analysis

1

Via link to an external website, top 500 genes passed via URL.